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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 5

Reclassification of as comb. nov. based on phylogenomics and multiple molecular synapomorphies No Access

Abstract

The taxonomic assignment of together with the in-house environmental isolate EB93 was reassessed in this study using phylogenetic and phylogenomic approaches, and the detection of multiple molecular synapomorphies. Results from the reconstructed phylogenetic trees based on the 16S rRNA gene sequences, the concatenated protein sequences of , and the whole-genome sequences revealed the consistent exclusion of and the environmental isolate EB93 from the cluster formed by the type strains of the genus . In addition, and the environmental isolate EB93 were both observed to form a clade together with the type strains of the genus . The results from the analysis of the digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the difference in the G+C content also corroborated with the phylogenetic inference, and that and the environmental isolate EB93 were of the same species. Furthermore, the presence of the molecular synapomorphies in the protein sequences noted in the description of the genus were also observed in , further strengthening its taxonomic affiliation in the genus. Based on the evidence from the multiple lines of analyses, we propose the reclassification of as a member of the genus and assume the name comb. nov. (type strain DSM 8801 =ATCC 25097=CCUG 43489=CIP 67.20=JCM 11681).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Brevibacterium , multiple molecular synapomorpies , Peribacillus , Peribacillus frigoritolerans comb. nov. and phylogenomics
Funding
This study was supported by the:
  • Yeungnam University (Award 221A380005)
    • Principle Award Recipient: HanhongBae
© 2022 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.005389
2022-05-23
2024-05-13
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References

  1. Salam N, Jiao J-Y, Zhang X-T, Li W-J. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
     [Google Scholar]
  2. Sneath PHA, McGOWAN V, Skerman VBD. Approved lists of bacterial names. Int J Syst Bacteriol 1980; 30:225–420 [View Article]
     [Google Scholar]
  3. Forquin-Gomez MP, Weimer BC, Sorieul L, Kalinowski J, Vallaeys T. The family Brevibacteriaceae. The Prokaryotes: Actinobacteria 2014; 141–153:
     [Google Scholar]
  4. Delaporte B, Sasson A. Study of bacteria from arid soils of morocco: Brevibacterium haloterans n. sp. and Brevibacterium frigoritolerans n. sp. comptes rendus hebd des seances l’Academie des. Sci Ser D Sci Nat 1967; 264:2257–2260
     [Google Scholar]
  5. Gelsomino R, Vancanneyt M, Vandekerckhove TM, Swings J. Development of a 16S rRNA primer for the detection of Brevibacterium spp. Lett Appl Microbiol 2004; 38:532–535 [View Article] [PubMed]
     [Google Scholar]
  6. Tindall BJ. The consequences of Bacillus axarquiensis Ruiz-García et al. 2005, Bacillus malacitensis Ruiz-García et al. 2005 and Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) being treated as heterotypic synonyms. Int J Syst Evol Microbiol 2017; 67:175–176 [View Article]
     [Google Scholar]
  7. Ben-Gad D, Gerchman Y. Reclassification of Brevibacterium halotolerans DSM8802 as Bacillus halotolerans comb. nov. based on microbial and biochemical characterization and multiple gene sequence. Curr Microbiol 2017; 74:1–5 [View Article]
     [Google Scholar]
  8. Ruiz-García C, Quesada E, Martínez-Checa F, Llamas I, Urdaci MC et al. Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain. Int J Syst Evol Microbiol 2005; 55:1279–1285 [View Article] [PubMed]
     [Google Scholar]
  9. Dunlap CA, Bowman MJ, Schisler DA, Rooney AP. Genome analysis shows Bacillus axarquiensis is not a later heterotypic synonym of Bacillus mojavensis; reclassification of Bacillus malacitensis and Brevibacterium halotolerans as heterotypic synonyms of Bacillus axarquiensis. Int J Syst Evol Microbiol 2016; 66:2438–2443 [View Article] [PubMed]
     [Google Scholar]
  10. Liu G-H, Liu B, Wang J-P, Che J-M, Li P-F. Reclassification of Brevibacterium frigoritolerans DSM 8801T as Bacillus frigoritolerans comb. nov. based on genome analysis. Curr Microbiol 2020; 77:1916–1923 [View Article] [PubMed]
     [Google Scholar]
  11. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  12. Oren A, Garrity GM, Parte AC. Why are so many effectively published names of prokaryotic taxa never validated?. Int J Syst Evol Microbiol 2018; 68:2125–2129 [View Article] [PubMed]
     [Google Scholar]
  13. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
     [Google Scholar]
  14. Ponpandian LN, Rim SO, Shanmugam G, Jeon J, Park Y-H et al. Phylogenetic characterization of bacterial endophytes from four Pinus species and their nematicidal activity against the pine wood nematode. Sci Rep 2019; 9:1–11 [View Article] [PubMed]
     [Google Scholar]
  15. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  16. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  18. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8:275–282 [View Article]
     [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article] [PubMed]
     [Google Scholar]
  21. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:141 [View Article] [PubMed]
     [Google Scholar]
  22. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  23. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  24. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1 [View Article]
     [Google Scholar]
  25. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
     [Google Scholar]
  26. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  27. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  28. Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000; 28:1102–1104 [View Article] [PubMed]
     [Google Scholar]
  29. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  30. La Duc MT, Satomi M, Agata N, Venkateswaran K. gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group. J Microbiol Methods 2004; 56:383–394 [View Article] [PubMed]
     [Google Scholar]
  31. Ki JS, Zhang W, Qian PY. Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. J Microbiol Methods 2009; 77:48–57 [View Article] [PubMed]
     [Google Scholar]
  32. Gupta RS, Lorenzini E. Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol 2007; 7:1–18 [View Article] [PubMed]
     [Google Scholar]
  33. Gupta RS, Mahmood S, Adeolu M. A phylogenomic and molecular signature based approach for characterization of the phylum spirochaetes and its major clades: proposal for a taxonomic revision of the phylum. Front Microbiol 2013; 0:217
     [Google Scholar]
  34. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  36. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
     [Google Scholar]
  37. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005; 21:2329–2335 [View Article] [PubMed]
     [Google Scholar]
  38. Holland BR, Huber KT, Dress A, Moulton V. Delta plots: A tool for analyzing phylogenetic distance data. Mol Biol Evol 2002; 19:2051–2059 [View Article] [PubMed]
     [Google Scholar]
  39. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  40. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  41. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:141 [View Article] [PubMed]
     [Google Scholar]
  42. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:1–8 [View Article] [PubMed]
     [Google Scholar]
  43. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  44. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  45. Heyrman J, Logan NA, Rodríguez-Díaz M, Scheldeman P, Lebbe L et al. Study of mural painting isolates, leading to the transfer of “Bacillus maroccanus” and “Bacillus carotarum” to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to “Bacillus macroides” and description of Bacillus muralis sp. nov. Int J Syst Evol Microbiol 2005; 55:119–131 [View Article] [PubMed]
     [Google Scholar]
  46. Gao B, Gupta RS. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 2012; 76:66–112 [View Article] [PubMed]
     [Google Scholar]
  47. Hu D, Zang Y, Mao Y, Gao B. Identification of molecular markers that are specific to the class Thermoleophilia. Front Microbiol 2019; 10:1185 [View Article] [PubMed]
     [Google Scholar]
  48. Gupta RS. Identification of conserved indels that are useful for classification and evolutionary studies. Methods Microbiol 2014; 41:153–182
     [Google Scholar]
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Reclassification of Brevibacterium frigoritolerans as Peribacillus frigoritolerans comb. nov. based on phylogenomics and multiple molecular synapomorphies
Int J Syst Evol Microbiol 72, 005389 (2022); https://doi.org/10.1099/ijsem.0.005389
/content/journal/ijsem/10.1099/ijsem.0.005389
/content/journal/ijsem/10.1099/ijsem.0.005389
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